ArticleeLife2026
Concerted changes in the pediatric single-cell intestinal ecosystem before and after anti-TNF blockade.
Abstract read
In one paragraph
Article in eLife, 2026. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 10 papers.
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10citing papers in PubMed
–field-weighted citation impact
What it found
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Who cites it
10 citing papers in PubMed.
- Article
- Divergent T Cell Phenotypes Define Pediatric Crohn's Disease and Ulcerative Colitis.medRxiv : the preprint server for health sciences · 2025Article
- Article
- scExtract: leveraging large language models for fully automated single-cell RNA-seq data annotation and prior-informed multi-dataset integration.Genome biology · 2025Article
- Article
- Variants and vaccines impact nasal immunity over three waves of SARS-CoV-2.Nature immunology · 2025Article
- Enteric glia regulate Paneth cell secretion and intestinal microbial ecology.bioRxiv : the preprint server for biology · 2024Article
- Article
- Article
- Primary nasal viral infection rewires the tissue-scale memory response.bioRxiv : the preprint server for biology · 2024Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
46 authors.
Hengqi Betty Zheng *Division of Gastroenterology and Hepatology, Seattle Children's Hospital and University of Washington, Seattle, United States.ORCID https://orcid.org/0000-0003-0575-6475
Benjamin A Doran *Division of Pediatric Hematology/Oncology, Boston Children's Hospital, Boston, United States.
Kyle Kimler *Division of Pediatric Hematology/Oncology, Boston Children's Hospital, Boston, United States.
Alison Yu *Division of Pediatric Hematology/Oncology, Boston Children's Hospital, Boston, United States.
Victor TkachevDivision of Pediatric Hematology/Oncology, Boston Children's Hospital, Boston, United States.
Veronika NiederlovaDivision of Gastroenterology, Hepatology, and Nutrition, Boston Children's Hospital, Boston, United States.
Kayla CribbinDivision of Pediatric Hematology/Oncology, Boston Children's Hospital, Boston, United States.
Ryan FlemingDivision of Pediatric Hematology/Oncology, Boston Children's Hospital, Boston, United States.
Brandi BratrudeDivision of Pediatric Hematology/Oncology, Boston Children's Hospital, Boston, United States.
Kayla BetzDivision of Pediatric Hematology/Oncology, Boston Children's Hospital, Boston, United States.
Lorenzo CagninDivision of Pediatric Hematology/Oncology, Boston Children's Hospital, Boston, United States.
Connor McGuckinDivision of Pediatric Hematology/Oncology, Boston Children's Hospital, Boston, United States.
Paula KeskulaDivision of Pediatric Hematology/Oncology, Boston Children's Hospital, Boston, United States.
Alexandre AlbaneseDivision of Pediatric Hematology/Oncology, Boston Children's Hospital, Boston, United States.
Maria SactaDivision of Gastroenterology, Hepatology, and Nutrition, Boston Children's Hospital, Boston, United States.
Joshua de Sousa CasalDivision of Gastroenterology, Hepatology, and Nutrition, Boston Children's Hospital, Boston, United States.
Ruben van EschUMC Utrecht, Utrecht, Netherlands.
Andrew C KwongDivision of Gastroenterology, Hepatology, and Nutrition, Boston Children's Hospital, Boston, United States.
Conner KummerloweInstitute for Medical Engineering & Science, Massachusetts Institute of Technology, Cambridge, United States.
Faith TaliaferroDivision of Gastroenterology, Hepatology, and Nutrition, Boston Children's Hospital, Boston, United States.
Nathalie FiaschiRegeneron Pharmaceuticals Inc, Tarrytown, United States.
Baijun KouRegeneron Pharmaceuticals Inc, Tarrytown, United States.
Sandra CoetzeeRegeneron Pharmaceuticals Inc, Tarrytown, United States.
Sumreen JalalRegeneron Pharmaceuticals Inc, Tarrytown, United States.
Yoko YabeRegeneron Pharmaceuticals Inc, Tarrytown, United States.
Michael DoboszRegeneron Pharmaceuticals Inc, Tarrytown, United States.
Matthew F WippermanRegeneron Pharmaceuticals Inc, Tarrytown, United States.ORCID https://orcid.org/0000-0003-1436-3366
Sara C HamonRegeneron Pharmaceuticals Inc, Tarrytown, United States.
George D KallioliasRegeneron Pharmaceuticals Inc, Tarrytown, United States.
Andrea HooperRegeneron Pharmaceuticals Inc, Tarrytown, United States.
Wei Keat LimRegeneron Pharmaceuticals Inc, Tarrytown, United States.ORCID https://orcid.org/0000-0002-6226-2570
Sokol HaxhinastoRegeneron Pharmaceuticals Inc, Tarrytown, United States.
Yi WeiRegeneron Pharmaceuticals Inc, Tarrytown, United States.
Madeline FordDivision of Gastroenterology and Hepatology, Seattle Children's Hospital and University of Washington, Seattle, United States.
Lusine AmbartsumyanDivision of Gastroenterology and Hepatology, Seattle Children's Hospital and University of Washington, Seattle, United States.
David L SuskindDivision of Gastroenterology and Hepatology, Seattle Children's Hospital and University of Washington, Seattle, United States.
Dale LeeDivision of Gastroenterology and Hepatology, Seattle Children's Hospital and University of Washington, Seattle, United States.
Gail H DeutschDepartment of Pathology, Seattle Children's Hospital and University of Washington, Seattle, United States.
Xuemei DengDepartment of Pathology, Seattle Children's Hospital and University of Washington, Seattle, United States.
Lauren V CollenDivision of Gastroenterology, Hepatology, and Nutrition, Boston Children's Hospital, Boston, United States.ORCID https://orcid.org/0000-0002-7769-8123
Vanessa MitsialisDivision of Gastroenterology, Hepatology, and Nutrition, Boston Children's Hospital, Boston, United States.
Scott B SnapperDivision of Gastroenterology, Hepatology, and Nutrition, Boston Children's Hospital, Boston, United States.
Ghassan WahbehDivision of Gastroenterology and Hepatology, Seattle Children's Hospital and University of Washington, Seattle, United States.
Alex K Shalek *Institute for Medical Engineering & Science, Massachusetts Institute of Technology, Cambridge, United States.
Jose Ordovas-Montanes *Division of Gastroenterology, Hepatology, and Nutrition, Boston Children's Hospital, Boston, United States.ORCID https://orcid.org/0000-0001-5444-5601
Leslie S Kean *Division of Pediatric Hematology/Oncology, Boston Children's Hospital, Boston, United States.ORCID https://orcid.org/0000-0003-0475-3926
Funding
Transplant Tolerance in Non-Human PrimatesU19AI051731 · NIAID · UNIVERSITY OF WESTERN ONTARIO · PI LARSEN, CHRISTIAN P. · 2002 to 2022
$54.1MSTRUCTURE-FUNCTION RELATIONSHIPS IN THE ALIMENTARY TRACTP30DK034854 · NIDDK · HARVARD UNIVERSITY (MEDICAL SCHOOL) · PI LYNN BRY · 1986 to 2026
$32.4MNovel Biologic Therapies for GVHDR01HL095791 · NHLBI · SEATTLE CHILDREN'S HOSPITAL · PI KEAN, LESLIE S · 2010 to 2025
$13.3MProject 3: Enhanced Costimulation Blockade to Achieve Clinically Relevant Heart Allograft ToleranceP01HL158504 · NHLBI · MASSACHUSETTS GENERAL HOSPITAL · PI MADSEN, JOREN C · 2021 to 2025
$12.1MIdentifying Immune and Epithelial Network Signatures in Very Early Onset Inflammatory Bowel DiseaseRC2DK122532 · NIDDK · BOSTON CHILDREN'S HOSPITAL · PI KLEIN, CHRISTOPH, MUISE, ALEIXO M · 2020 to 2024
$9.1MOptimizing HCT Outcomes: A Multi-omic InvestigationR01HL181969 · NHLBI · BOSTON CHILDREN'S HOSPITAL · PI Ami Siddharth Bhatt, Leslie S Kean · 2025 to 2026
$3.9MAn integrated multiplexed genomic assay for low input clinical samples1U24AI118672 · NIAID · BROAD INSTITUTE, INC. · PI SHALEK, ALEX K · 2015 to 2019
$2.0MAGA Research Foundation AGA2020-13-01Harvard Digestive Diseases Center, Harvard University DK034854International mobility of research, technical and administrative staff of research organizations CZ.02.2.69/0.0/0.0/18_053/0016981National Institute of Health NIH/NHLBI R01 HL095791National Institute of Health NIH/NHLBI R01 HL181969National Institute of Health P01 1P01HL158504National Institute of Health R01 5R01HL095791National Institute of Health U19 U19AI051731NHLBI NIH HHS 2R01HL095791NHLBI NIH HHS P01 HL158504NHLBI NIH HHS R01 HL095791NHLBI NIH HHS R01 HL181969NIAID NIH HHS 5U24AI118672NIAID NIH HHS U19 AI051731NIAID NIH HHS U24 AI118672NIDDK NIH HHS P30 DK034854NIDDK NIH HHS RC2 DK122532
Abstract
Crohn's disease is an inflammatory bowel disease (IBD) commonly treated through anti-TNF blockade. However, most patients still relapse and inevitably progress. Comprehensive single-cell RNA-sequencing (scRNA-seq) atlases have largely sampled patients with established treatment-refractory IBD, limiting our understanding of which cell types, subsets, and states at diagnosis anticipate disease severity and response to treatment. Here, through combining clinical, flow cytometry, histology, and scRNA-seq methods, we profile diagnostic human biopsies from the terminal ileum of treatment-naive pediatric patients with Crohn's disease (pediCD;
Indexed as
Crohn DiseaseTumor Necrosis Factor-alphaTumor Necrosis Factor InhibitorsAdolescentChildFemaleHumansIleumIntestinal MucosaMaleSingle-Cell AnalysisSingle-Cell Gene Expression AnalysisTumor Necrosis Factor-alphaTumor Necrosis Factor Inhibitorsanti-TNFCrohn's diseasehumanimmunologyinflammationmedicinepediatricscRNA-seqtissue atlas
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.